Winter wheat can regrow surviving the cold winter in extremely cold areas and this type of cold resistance is a very attractive quality. Very little is known regarding the molecular mechanism of cold resistance in winter wheat, particularly the identity of the cold resistance genes. In this study, RNA was extracted from the crown of winter wheat varieties with different cold resistances subjected to various low-temperature treatments. Using the Solexa/Illumina sequencing platform, 60 million sequencing reads were obtained and these reads were assembled into 80, 704 unigenes. Based on the method of known protein similarity search, we acquired 51, 929 sequences that were consistent with the standard E-value cut-off of 10-5. Additionally, 22, 724 sequences were annotated by gene ontology (GO) term, 31, 964 sequences were annotated by Swiss-Prot, 18, 764 sequences were clustered into 43 types by Clusters of Orthologous Groups classifications (COG) and 29, 553 sequences are assigned to 125 pathways by the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG). Furthermore, transcription factor genes involved in cold and dehydration resistance are more highly expressed in Dongnongdongmai 1, which is cold resistant, compared to Jimai 22, which is cold sensitive. The expression of genes in Phenylalanine metabolism, Alpha-linolenic acid metabolism, Gluathione metabolism, as well as Starch and sucrose metabolism pathway was triggered by LT. In addition, these pathways had difference between the two winter wheat varieties. We performed cluster analysis for the differentially expressed genes. Eight genes were randomly selected for expression quantity validation by quantitative RT-PCR. These results of the gene expression pattern analysis under three low temperature treatments are essentially same as the DGE data. Summarily, we obtained an extensive transcriptome dataset from winter wheat, a non-model whole genome which identifies winter wheat cold resistance genes under low temperature conditions.
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